[R] checkConv and as.data.frame.default problems in R

Saudi Sadiq ss1272 at york.ac.uk
Thu Jul 2 12:58:38 CEST 2015 

Hi Jon,
Thanks for your reply. I will try again, after correcting mistakes. Then,
if the model does not converge, I will come back to you with datasets
attached.
Best

On 1 July 2015 at 21:01, John Fox <jfox at mcmaster.ca> wrote:

> Dear Saudi Sadiq,
>
> If you want answers to most of your questions, you'll likely have to
> provide your data so that people can reproduce the errors. I can, however,
> answer part of your last question without the data:
>
> plot(allEffects(modelqaaf1)) fails because the data set is named q, and
> there is a standard R function named q(). Obviously there is a scoping
> issue that confuses allEffects() for a reason I don't yet understand.
>
> Here's a simple example that reproduces this error:
>
> ---------- snip ------------
>
> > library(lme4)
> Loading required package: Matrix
> Loading required package: Rcpp
> > library(effects)
> > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake)
> > allEffects(fm1)
>  model: angle ~ recipe * temperature
>
>  recipe*temperature effect
>       temperature
> recipe      175      185      195      205      215      225
>      A 29.13333 31.53333 30.80000 33.53333 38.66667 35.06667
>      B 26.86667 29.40000 31.73333 32.13333 34.46667 35.26667
>      C 27.93333 28.93333 31.73333 30.86667 34.40000 35.73333
> > q <- cake
> > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), data=q)
> > allEffects(fm1)
>
>  Error in as.data.frame.default(data, optional = TRUE) :
>   cannot coerce class ""function"" to a data.frame
>
> ------------- snip -------------
>
> Why, as you claim, you get the same error with
> plot(allEffects(modelqaaf)), where the data set is qaaf rather than q, is
> hard to understand, and perhaps you're mistaken.
>
> I hope this helps,
>  John
>
> ------------------------------------------------
> John Fox, Professor
> McMaster University
> Hamilton, Ontario, Canada
> http://socserv.mcmaster.ca/jfox/
>
>
> On Wed, 1 Jul 2015 15:40:48 +0100
>  Saudi Sadiq <ss1272 at york.ac.uk> wrote:
> > Hi All,
> >
> > I have two datasets, vowels and qaaf, and both have 8 columns clarified
> as
> > follows:
> >
> > 1.  convergence: DV (whether participants succeeded to use CA (Cairene
> > Arabic) or fail to do so; hence, they use MA (Minia Arabic)
> >
> > 2.  speaker: 62 participants
> >
> > 3.  lexical.item: as pronounced
> >
> > 4.  style: careful and casual
> >
> > 5.  gender: males and females
> >
> > 6.  age: continues variable
> >
> > 7.  residence: urbanite, migrant to town or villager
> >
> > 8.  education: secondary or below, university or postgraduate
> >
> > The only difference between the two datasets is the number of items. With
> > the vowels dataset, there are 1339 items; in the qaaf dataset there are
> > 4064 items.
> >
> > The aim of the test done was to know which independent variable is more
> > responsible for using CA forms. I used the lme4 package, function glmer.
> >
> > I ran the model:
> >
> > 1.  modelvowels <- glmer(convergence ~ gender + age + residence +
> > education +  style+ (1|lexical.item) + (1|speaker), data=vowels,
> > family='binomial')
> >
> > The message came on the screen:
> >
> > 2.  Warning message:
> >
> > In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
> >
> >   Model failed to converge with max|grad| = 0.00210845 (tol = 0.001,
> > component 1)
> >
> > Then I ran the model after removing STYLE as follows:
> >
> > 3.  modelvowels <- glmer(convergence ~ gender + age + residence +
> > education + (1|lexical.item) + (1|speaker), data=vowels,
> > family='binomial')
> >
> > This produced a result. Then, I ran
> >
> > 4.  plot(allEffects(modelvowels))
> >
> >
> >
> > and this gave four charts (for the four independent variables: gender,
> age,
> > residence and education).
> >
> > Then, I moved to the qaaf dataset (4064 items) and ran the same model
> >
> > 5.  modelqaaf <- glmer(convergence ~ gender + age + residence +
> > education + (1|lexical.item) + (1|speaker), data=qaaf,
> > family='binomial')
> >
> > which gave results with the vowels dataset but there was a warning
> message
> > this time
> >
> > 6.  Warning message:
> >
> > In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
> >
> >   Model failed to converge with max|grad| = 0.429623 (tol = 0.001,
> component 8)
> >
> > So, I removed one independent variable (residence) and ran this model
> again:
> >
> > 7.  modelqaaf <- glmer(convergence ~ gender + age + education +
> > (1|lexical.item) + (1|speaker), data=qaaf, family='binomial')
> >
> > This gave a result. I removed another independent variable (gender) after
> > returning (residence) and ran the model:
> >
> > 8.  modelqaaf1 <- glmer(convergence ~ residence + age + education +
> > (1|lexical.item) + (1|speaker), data=q, family='binomial')
> >
> > This gave a result as well. Then, I tried to create some graphs using
> >
> > 9.  plot(allEffects(modelqaaf)) and
> >
> > 10. plot(allEffects(modelqaaf1))
> >
> >
> >
> > but there was the same error for both
> >
> > 11. Error in as.data.frame.default(data, optional = TRUE) :
> >
> >   cannot coerce class ""function"" to a data.frame
> >
> >  Now, my questions:
> >
> > a.  why 1 did not work, why 3 worked, why 5 did not work though it has
> > the same four IVs of 3, why 7 and 8 worked with only three IVs, and
> > why 9 and 10 did not work though they are like 4 which worked well.
> >
> >
> >
> > b.  What are the packages that must be installed with, before or after
> > the lme4 package?
> >
> >
> >
> >  Best
> >
> > --
> > Saudi Sadiq,
> > Assistant Lecturer, English Department,
> > Faculty of Al-Alsun,Minia University,
> > Minia City, Egypt &
> > PhD Student, Language and Linguistic Science Department,
> > University of York, York, North Yorkshire, UK,
> > YO10 5DD
> > http://york.academia.edu/SaudiSadiq
> > https://www.researchgate.net/profile/Saudi_Sadiq
> > Certified Interpreter by Pearl Linguistics
> >
> > Forum for Arabic Linguistics conference ???? ???????
> > 28-30th July 2015 - call for papers now open
> > https://sites.google.com/a/york.ac.uk/fal2015/
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
>


-- 
Saudi Sadiq,
Assistant Lecturer, English Department,
Faculty of Al-Alsun,Minia University,
Minia City, Egypt &
PhD Student, Language and Linguistic Science Department,
University of York, York, North Yorkshire, UK,
YO10 5DD
http://york.academia.edu/SaudiSadiq
https://www.researchgate.net/profile/Saudi_Sadiq
Certified Interpreter by Pearl Linguistics

Forum for Arabic Linguistics conference رواق العربية
28-30th July 2015 - call for papers now open
https://sites.google.com/a/york.ac.uk/fal2015/

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